Variant report

Variant	rs248944
Chromosome Location	chr19:19887174-19887175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19886626-19887863	H1-neurons	neurons:	n/a	n/a
2	GABPA	chr19:19887046-19887983	SK-N-SH	brain:	n/a	n/a
3	ELF1	chr19:19886995-19887890	GM12878	blood:	n/a	n/a
4	MAX	chr19:19887098-19887879	H1-hESC	embryonic stem cell:	n/a	chr19:19887863-19887872 chr19:19887227-19887237
5	MAX	chr19:19886698-19887967	ECC-1	luminal epithelium:	n/a	chr19:19887863-19887872 chr19:19887227-19887237
6	TAF1	chr19:19886961-19887759	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:19886998-19887811	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:19886875-19887892	GM12891	blood:	n/a	n/a
9	ETS1	chr19:19887065-19887642	A549	lung:	n/a	chr19:19887315-19887328 chr19:19887320-19887327 chr19:19887316-19887329 chr19:19887265-19887278
10	PAX5	chr19:19887093-19887710	GM12878	blood:	n/a	n/a
11	PML	chr19:19887013-19887594	K562	blood:	n/a	n/a
12	POU2F2	chr19:19887022-19887360	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:19886833-19887979	GM12878	blood:	n/a	n/a
14	IRF1	chr19:19887061-19887654	K562	blood:	n/a	n/a
15	CREB1	chr19:19886807-19887953	HepG2	liver:	n/a	n/a
16	CREB1	chr19:19886857-19887784	H1-hESC	embryonic stem cell:	n/a	n/a
17	SIX5	chr19:19887021-19887740	GM12878	blood:	n/a	chr19:19887319-19887328 chr19:19887545-19887554 chr19:19887317-19887326 chr19:19887406-19887415 chr19:19887268-19887277
18	MAX	chr19:19886907-19887930	HCT-116	colon:	n/a	chr19:19887863-19887872 chr19:19887227-19887237
19	TEAD4	chr19:19887056-19887542	K562	blood:	n/a	n/a
20	MAFF	chr19:19887081-19887957	K562	blood:	n/a	n/a
21	POLR2A	chr19:19886981-19887712	HepG2	liver:	n/a	n/a
22	SP1	chr19:19886981-19887702	A549	lung:	n/a	chr19:19887227-19887241 chr19:19887353-19887367 chr19:19887619-19887633 chr19:19887352-19887363 chr19:19887041-19887062
23	GABPA	chr19:19887064-19887680	K562	blood:	n/a	n/a
24	TAF1	chr19:19887004-19887782	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr19:19886966-19887752	HUVEC	blood vessel:	n/a	n/a
26	TCF12	chr19:19887098-19887528	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:19886790-19887859	HepG2	liver:	n/a	n/a
28	FOS	chr19:19887170-19887660	MCF10A-Er-Src	breast:	n/a	n/a
29	SIN3AK20	chr19:19887053-19887301	SK-N-SH	brain:	n/a	n/a
30	CREB1	chr19:19886896-19887723	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:19887017-19887286	K562	blood:	n/a	n/a
32	ETS1	chr19:19887016-19887705	GM12878	blood:	n/a	chr19:19887315-19887328 chr19:19887320-19887327 chr19:19887316-19887329 chr19:19887265-19887278
33	POLR2A	chr19:19886856-19888109	Hela-S3	cervix:	n/a	n/a
34	EGR1	chr19:19887010-19887767	HCT-116	colon:	n/a	chr19:19887380-19887393 chr19:19887455-19887479 chr19:19887316-19887340
35	RAD21	chr19:19887134-19887786	H1-hESC	embryonic stem cell:	n/a	n/a
36	ELK1	chr19:19887057-19887856	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr19:19886933-19887868	GM12892	blood:	n/a	n/a
38	POLR2A	chr19:19886975-19887776	K562	blood:	n/a	n/a
39	MYC	chr19:19887083-19887867	NB4	blood:	n/a	chr19:19887227-19887237
40	STAT1	chr19:19886632-19887816	GM12878	blood:	n/a	chr19:19886772-19886792 chr19:19887349-19887361 chr19:19886772-19886792 chr19:19887223-19887235
41	CREB1	chr19:19886984-19887725	K562	blood:	n/a	n/a
42	SMC3	chr19:19887082-19887858	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:19887003-19887641	HUVEC	blood vessel:	n/a	n/a
44	GABPA	chr19:19887125-19887521	K562	blood:	n/a	n/a
45	ELF1	chr19:19887168-19887814	HepG2	liver:	n/a	n/a
46	SIN3AK20	chr19:19886924-19888040	SK-N-SH	brain:	n/a	n/a
47	MAX	chr19:19886987-19887794	K562	blood:	n/a	chr19:19887227-19887237
48	SP1	chr19:19887011-19887695	HepG2	liver:	n/a	chr19:19887227-19887241 chr19:19887353-19887367 chr19:19887619-19887633 chr19:19887352-19887363 chr19:19887041-19887062
49	MAX	chr19:19887030-19887825	HepG2	liver:	n/a	chr19:19887227-19887237
50	STAT5A	chr19:19887093-19887934	GM12878	blood:	n/a	chr19:19887349-19887361 chr19:19887223-19887235

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19772600..19774395-chr19:19886060..19888388,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF506-1	chr19:19887136-19887189	ENSG00000228642
2	lnc-ZNF506-1	chr19:19887132-19887185	ENSG00000266904.1
3	lnc-ZNF506-1	chr19:19887136-19887801	NONHSAT063584
4	lnc-ZNF506-1	chr19:19887136-19887222	ENSG00000266904.1
5	lnc-ZNF506-1	chr19:19884687-19887232	ENSG00000266904.1
6	lnc-ZNF506-1	chr19:19887136-19887189	ENSG00000266904.1
7	lnc-ZNF506-1	chr19:19887136-19887202	ENSG00000228642
8	lnc-ZNF506-1	chr19:19887136-19887194	ENSG00000266904.1
9	lnc-ZNF506-1	chr19:19887132-19887203	ENSG00000266904.1

Variant related genes	Relation type
ENSG00000267419	TF binding region
ENSG00000105726	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10404296	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10412885	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12710110	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs16996360	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248930	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248931	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248932	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248933	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248934	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248936	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248937	0.82[EUR][1000 genomes]
rs248942	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248948	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248949	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248951	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248952	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248954	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762190	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808216	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4808989	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4808991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808995	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6511050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246727	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256535	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8106100	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8109240	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111421	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911312	chr19:19861682-19917662	Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv458375	chr19:19863014-19949209	Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv578798	chr19:19863014-19949209	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv911313	chr19:19866371-19936078	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs248944	ZNF506	cis	normal skin	skin_eQTL
rs248944	LINC00663	cis	Artery Tibial	GTEx
rs248944	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19886000-19888000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:19886200-19887800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr19:19886200-19887800	Active TSS	Fetal Brain Male	brain
4	chr19:19886200-19888400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr19:19886200-19888400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:19886200-19888600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr19:19886200-19888600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19886200-19888600	Active TSS	A549	lung
9	chr19:19886400-19887200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr19:19886400-19887200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr19:19886400-19887800	Active TSS	Fetal Brain Female	brain
12	chr19:19886400-19888000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:19886400-19888000	Active TSS	Esophagus	oesophagus
14	chr19:19886400-19888200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:19886400-19888400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr19:19886400-19888400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:19886400-19888400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:19886400-19888400	Active TSS	Fetal Muscle Trunk	muscle
19	chr19:19886400-19888400	Active TSS	Pancreas	Pancrea
20	chr19:19886400-19888600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:19886400-19888600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:19886400-19888600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:19886400-19888800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr19:19886400-19889000	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr19:19886600-19887200	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr19:19886600-19887200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
27	chr19:19886600-19887800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:19886600-19887800	Active TSS	Brain Angular Gyrus	brain
29	chr19:19886600-19887800	Active TSS	Fetal Lung	lung
30	chr19:19886600-19887800	Active TSS	Placenta Amnion	Placenta Amnion
31	chr19:19886600-19888000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:19886600-19888000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:19886600-19888000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:19886600-19888000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:19886600-19888000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr19:19886600-19888000	Active TSS	Brain Cingulate Gyrus	brain
37	chr19:19886600-19888000	Active TSS	Brain Hippocampus Middle	brain
38	chr19:19886600-19888000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:19886600-19888000	Active TSS	Colon Smooth Muscle	Colon
40	chr19:19886600-19888000	Active TSS	Fetal Intestine Large	intestine
41	chr19:19886600-19888000	Active TSS	Fetal Kidney	kidney
42	chr19:19886600-19888000	Active TSS	Left Ventricle	heart
43	chr19:19886600-19888000	Active TSS	Lung	lung
44	chr19:19886600-19888000	Active TSS	Ovary	ovary
45	chr19:19886600-19888000	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:19886600-19888000	Active TSS	Right Atrium	heart
47	chr19:19886600-19888000	Active TSS	Stomach Mucosa	stomach
48	chr19:19886600-19888200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:19886600-19888200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:19886600-19888200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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